Funny thing is that I also had the same problem with setting up a 80 GB harddisk on my A1200, where HDToolBox would only show ca. 18 GB. My solution was to first use the AmigaOS 3.1 version of HDToolBox for installing the harddisk, then I booted the AmigaOS 3.9 CD and did the rest from HDToolBox there. After that I was able to use the full 80 GB of the harddisk.
I belive there is a bug somewhere on the AmigaOS 3.9 CD which causes this type of problems.
